Up: Component summary Component

ExonToPeptide

Fetches exon-peptide sequences of query exon list.

Version 1.0
Bundle microarray
Categories Exon
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires Ensembl Perl API
Source files component.xml ExonToPeptide.pl
Usage Example with default values

Inputs

Name Type Mandatory Description
ExonList CSV Mandatory A CSV file contains a column of query exon Ensembl IDs. The first row should be headers.
connection Properties Mandatory Connection parameters of Ensembl database, including host, database, port, user and driver information.

Outputs

Name Type Description
ExonSeq FASTA A fasta format file for exon sequences.
PeptideSeq FASTA A fasta format file for peptide sequences of query exons.

Parameters

Name Type Default Description
ExonColumn int (no default) The index of column containing exon Ensembl IDs in input ExonList file.
SeqType string "both" Output sequence type of interest. It can be "exon-only", "peptide-only" or "both".
remove boolean true Remove unmatched records from results. The default value is "true".
version int (no default) Ensembl database version number. After version 66, the database schema has changed. Thus, please make sure you enter the correct version number.

Test cases

Test case Parameters IN
ExonList
IN
connection
OUT
ExonSeq
OUT
PeptideSeq
case1 properties ExonList connection ExonSeq PeptideSeq

ExonColumn=1,
SeqType=exon-only,
remove=true,
version=71

case2 properties ExonList connection ExonSeq PeptideSeq

ExonColumn=1,
SeqType=both,
remove=true,
version=71


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